Contacts of the helix formed by residues 151 - 167 (chain D) in PDB entry 5USJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 151 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D ILE* 4.1 4.3 - - - +
143D GLU 3.9 14.8 - - - -
144D THR* 3.6 7.0 - - - +
149D ARG 3.3 1.8 + - - -
150D GLN* 1.3 73.2 - - - +
152D VAL* 1.3 53.6 + - - +
153D ASP 3.6 1.6 - - - -
154D ASP* 3.5 15.3 - - - +
155D ALA* 2.7 37.8 + - - +
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Residues in contact with VAL 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.7 40.8 - - + +
22D GLN* 4.1 12.8 - - + -
23D LEU* 3.9 24.9 - - + +
144D THR* 4.8 2.9 - - - -
145D SER 3.7 19.5 - - - +
146D ALA* 4.3 0.4 - - - -
149D ARG* 3.4 30.5 + - + +
150D GLN 3.1 4.7 + - - +
151D GLY* 1.3 75.7 - - - +
153D ASP* 1.3 67.8 + - - +
155D ALA* 3.2 7.9 + - - +
156D PHE* 3.2 23.9 - - + -
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Residues in contact with ASP 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 3.2 26.0 - - - +
42D LYS* 4.4 4.2 + - - -
149D ARG* 3.1 33.9 + - - +
152D VAL* 1.3 75.1 - - - +
154D ASP* 1.3 58.2 + - - +
156D PHE* 3.1 3.3 + - - -
157D TYR* 2.9 62.1 + - + -
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Residues in contact with ASP 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ILE* 3.9 18.6 - - + +
151D GLY* 3.3 18.5 + - - +
152D VAL 3.2 0.4 - - - -
153D ASP* 1.3 80.9 - - - +
155D ALA* 1.3 56.6 + - - +
157D TYR* 4.5 4.9 - - - -
158D THR* 2.7 51.5 + - - -
161D ARG* 4.5 6.6 + - - -
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 6.2 1.6 - - + -
79D LEU* 3.5 23.0 - - + +
112D VAL* 4.4 1.4 - - - +
114D VAL* 4.2 21.3 - - + -
142D ILE* 3.5 14.8 - - + +
144D THR* 4.2 15.5 - - + -
151D GLY 2.7 20.5 + - - +
152D VAL* 3.2 6.0 + - - +
154D ASP* 1.3 73.5 - - - +
156D PHE* 1.3 62.4 + - + +
158D THR* 4.0 1.7 - - - -
159D LEU* 3.2 15.8 + - - +
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Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 4.0 22.0 - - + +
8D VAL* 4.2 4.0 - - + -
19D LEU* 4.2 16.4 - - + -
20D THR* 4.1 22.2 - - - -
23D LEU* 3.8 42.2 - - + -
53D LEU* 4.7 7.2 - - + -
55D ILE* 4.0 25.8 - - + -
79D LEU* 3.7 28.7 - - + -
152D VAL* 3.2 24.2 - - + -
153D ASP 3.1 6.3 + - - +
155D ALA* 1.3 78.0 - - + +
157D TYR* 1.3 64.3 + - + +
159D LEU* 3.2 6.8 + - - +
160D VAL* 3.0 31.5 + - - +
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Residues in contact with TYR 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 5.1 3.6 - - + -
42D LYS* 5.3 2.4 + - - -
44D VAL* 4.3 24.2 - - + +
45D VAL 4.5 13.1 + - - -
46D ILE* 3.9 38.8 - - + +
53D LEU* 5.3 2.5 - - + -
153D ASP* 2.9 51.5 + - + +
154D ASP* 4.1 4.3 - - - +
156D PHE* 1.3 74.6 - - + +
158D THR* 1.3 66.7 + - - +
160D VAL* 3.2 4.0 + - - +
161D ARG* 3.0 49.1 + - - +
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Residues in contact with THR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D VAL* 4.0 3.8 - - + -
140D PRO* 3.7 35.4 - - + -
142D ILE* 3.5 15.6 - - + +
154D ASP* 2.7 39.0 + - - -
155D ALA 4.0 1.1 - - - -
157D TYR* 1.3 79.1 - - - +
159D LEU* 1.3 56.2 + - - +
161D ARG* 3.2 18.1 + - + +
162D GLU* 2.9 28.2 + - + +
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.9 27.6 - - + -
7D VAL 5.0 0.4 - - - +
77D GLY* 3.6 15.9 - - - +
78D PHE 3.6 48.0 - - - +
79D LEU* 3.9 13.9 - - + +
110D PRO* 3.9 15.9 - - + +
111D MET* 4.0 5.2 - - - +
112D VAL* 3.7 13.2 - - + +
155D ALA 3.2 13.8 + - - +
156D PHE* 3.2 10.1 + - - +
158D THR* 1.3 76.2 - - - +
160D VAL* 1.3 63.5 + - - +
162D GLU* 3.0 13.8 + - + +
163D ILE* 3.0 13.8 + - + +
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Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 3.7 31.2 - - + -
6D LEU* 4.3 8.3 - - + -
46D ILE* 3.7 23.1 - - + -
53D LEU* 3.6 30.5 - - + -
156D PHE 3.0 18.8 + - - +
157D TYR 3.2 7.2 + - - +
159D LEU* 1.3 76.4 - - - +
161D ARG* 1.3 62.9 + - - +
163D ILE* 3.1 10.8 + - - +
164D ARG* 2.9 39.9 + - - +
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Residues in contact with ARG 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ILE* 4.1 20.2 - - + +
47D ASP* 2.9 43.8 + - - +
154D ASP* 4.5 5.5 + - - -
157D TYR* 3.0 37.3 + - - +
158D THR* 3.2 24.7 + - + +
160D VAL* 1.3 78.0 - - - +
162D GLU* 1.3 63.9 + - - +
164D ARG* 3.5 12.3 + - - +
165D LYS* 3.2 30.0 + - + +
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PRO* 4.0 19.2 - - + +
111D MET 4.2 7.7 + - - +
112D VAL* 4.3 3.1 - - + -
138D GLY 4.6 8.0 - - - +
139D ILE* 4.8 1.2 - - - +
140D PRO* 3.7 38.8 - - + +
158D THR* 2.9 19.4 + - - +
159D LEU* 3.0 11.8 + - + +
161D ARG* 1.3 75.2 - - - +
163D ILE* 1.3 64.1 + - - +
165D LYS* 2.7 39.0 + - - +
166D HIS* 3.1 20.1 + - - +
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Residues in contact with ILE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 3.8 20.2 - - + -
6D LEU* 3.5 31.4 - - + -
76D GLU* 3.7 19.7 - - + +
77D GLY* 3.9 16.6 - - - +
110D PRO* 3.6 24.2 - - + -
159D LEU* 3.0 15.9 + - + +
160D VAL* 3.1 6.7 + - - +
162D GLU* 1.3 74.6 - - - +
164D ARG* 1.3 58.2 + - - +
166D HIS* 3.1 4.1 + - + +
167D LYS* 3.0 54.7 + - + +
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Residues in contact with ARG 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 3.0 27.1 + - + +
46D ILE* 2.8 38.6 + - - +
47D ASP* 4.0 12.1 + - - +
49D GLU* 2.9 52.4 + - - +
51D CYS* 4.0 13.7 - - - -
160D VAL* 2.9 25.7 + - - +
161D ARG* 3.7 9.7 - - - +
162D GLU 3.3 0.2 - - - -
163D ILE* 1.3 75.4 - - - +
165D LYS* 1.3 62.7 + - + +
167D LYS* 3.5 24.4 + - + +
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Residues in contact with LYS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ARG* 3.2 14.4 + - + +
162D GLU* 2.7 40.5 + - - +
163D ILE 3.3 0.4 - - - -
164D ARG* 1.3 77.1 - - + +
166D HIS* 1.3 65.9 + - - +
167D LYS 3.9 3.6 - - - +
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Residues in contact with HIS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D SER* 5.1 2.7 + - - -
108D ASP* 2.7 54.1 + - + +
110D PRO* 3.9 19.6 - - + +
162D GLU 3.1 11.7 + - - +
163D ILE* 3.1 9.9 + - + +
165D LYS* 1.3 77.4 - - - +
167D LYS* 1.3 70.0 + - + +
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Residues in contact with LYS 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D THR* 4.8 6.2 - - + +
3D GLU 4.1 6.7 + - - -
4D TYR* 3.5 27.1 - - + +
76D GLU* 3.0 28.4 + - - -
163D ILE* 3.0 32.1 + - + +
164D ARG* 3.5 17.8 + - + +
165D LYS 3.4 4.1 - - - +
166D HIS* 1.3 85.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il